A distance-type measure approach to the analysis of copy number variation in DNA sequencing data

Background

The next generation sequencing technology allows us to obtain a large amount of short DNA sequence (DNA-seq) reads at a genome-wide level. DNA-seq data have been increasingly collected during the recent years. Count-type data analysis is a widely used approach for DNA-seq data. However, the related data pre-processing is based on the moving window method, in which a window size need to be defined in order to obtain count-type data. Furthermore, useful information can be reduced after data pre-processing for count-type data.

Results

In this study, we propose to analyze DNA-seq data based on the related distance-type measure. Distances are measured in base pairs (bps) between two adjacent alignments of short reads mapped to a reference genome. Our experimental data based simulation study confirms the advantages of distance-type measure approach in both detection power and detection accuracy. Furthermore, we propose artificial censoring for the distance data so that distances larger than a given value are considered potential outliers. Our purpose is to simplify the pre-processing of DNA-seq data. Statistically, we consider a mixture of right censored geometric distributions to model the distance data. Additionally, to reduce the GC-content bias, we extend the mixture model to a mixture of generalized linear models (GLMs). The estimation of model can be achieved by the Newton-Raphson algorithm as well as the Expectation-Maximization (E-M) algorithm. We have conducted simulations to evaluate the performance of our approach. Based on the rank based inverse normal transformation of distance data, we can obtain the related z-values for a follow-up analysis. For an illustration, an application to the DNA-seq data from a pair of normal and tumor cell lines is presented with a change-point analysis of z-values to detect DNA copy number alterations.

Conclusion

Our distance-type measure approach is novel. It does not require either a fixed or a sliding window procedure for generating count-type data. Its advantages have been demonstrated by our simulation studies and its practical usefulness has been illustrated by an experimental data application.

     

Cytokine-mediated induction of human immunodeficiency virus (HIV) expression and cell death in chronically infected U1 cells: do tumor necrosis factor alpha and gamma interferon selectively kill HIV-infected cells?

Infection with several DNA or RNA viruses induces a state of increased sensitivity to cell lysis mediated by tumor necrosis factor (TNF), particularly in the presence of gamma interferon (IFN-gamma). Infection of human cells with the human immunodeficiency virus (HIV) may induce a similar phenomenon. However, TNF and IFN-gamma are known upregulators of HIV replication, raising the question of the potential role of these cytokines in the selective elimination of cells infected with this virus. The present study demonstrates that chronically infected U1 cells were killed with much greater efficiency by costimulation with TNF-alpha and IFN-gamma than their uninfected parental cell line U937. However, synergistic induction of viral expression also occurred in U1 cells as a consequence of treatment with the two cytokines. Cell death in U1 cells was not caused by the massive production of virions, in that costimulation with glucocorticoid hormones and TNF-alpha or IFN-gamma resulted in high levels of virion production without cytopathicity. To investigate the nature of the selective cytotoxic effect observed in U1 cells costimulated with TNF-alpha plus IFN-gamma, a panel of uninfected cell clones was generated by limiting dilution of U937 cells and tested for response to TNF-alpha and/or IFN-gamma. In contrast to the uncloned bulk parental U937 cell line, most uninfected cell clones showed a very high susceptibility to being killed by TNF-alpha and IFN-gamma. Similar findings were obtained when both infected U1 cells and several uninfected U937 cell clones were costimulated with an anti-Fas monoclonal antibody in the presence of IFN-gamma, although, unlike cells stimulated with TNF-alpha, cells treated with anti-Fas antibody did not express virus. Therefore, the increased susceptibility to cytokine-mediated lysis observed in cell lines infected with HIV is likely due to the selection of preexisting cell clones rather than viral infection.     

Ferulic acid (FA) abrogates γ-radiation induced oxidative stress and DNA damage by up-regulating nuclear translocation of Nrf2 and activation of NHEJ pathway

The present study was aimed to evaluate the radioprotective effect of ferulic acid (FA), a naturally occurring plant flavonoid in terms of DNA damage and damage related alterations of repair pathways by gamma radiation. FA was administered at a dose of 50?mg/kg body weight for five consecutive days prior to exposing the swiss albino mice to a single dose of 10?Gy gamma radiation. Ionising radiation induces oxidative damage manifested by decreased expression of Cu, Zn-SOD (SOD stands for super oxide dismutase), Mn-SOD and catalase. Gamma radiation promulgated reactive oxygen species (ROS) mediated DNA damage and modified repair pathways. ROS enhanced nuclear translocation of p53, activated ATM (ataxia telangiectasia-mutated protein), increased expression of GADD45a (growth arrest and DNA-damage-inducible protein) gene and inactivated Non homologous end joining (NHEJ) repair pathway. The comet formation in irradiated mice peripheral blood mononuclear cells (PBMC) reiterated the DNA damage in IR exposed groups. FA pretreatment significantly prevented the comet formation and regulated the nuclear translocation of p53, inhibited ATM activation and expression of GADD45a gene. FA promoted the nuclear translocation of nuclear factor (erythroid-derived 2)-like 2 (Nrf2) and activated NHEJ repair pathway to overcome ROS mediated oxidative stress and DNA damage. Therefore, the current study stated that FA can challenge the oxidative stress by (i) inducing nuclear translocation of Nrf2, (ii) scavenging ROS, and (iii) activating NHEJ DNA repair process.     

Effect of calcium on water-stress-induced biochemical changes and yield of field-grown rice

Three different treatments by calcium (10²M), namely seed treatment, foliar spraying and their combination were applied on field-grown rice (Oryza sativa L. cv. Ratna) under both water stressed and non-stressed conditions in the course of plant development. The relative water content and leaf water potential decreased with increase in age of stressed and non-stressed plants. Pretreatment of seeds with Ca improved the water status of the plants most prominently at the vegetative stage but the effect gradually faded away with plant development. The foliar spraying by Ca was more effective in improving the water status of the plants at the reproductive stage. The combined Ca treatment significantly improved water status of the plants both at the vegetative and reproductive stages. The contents of chlorophyll and protein decreased and the activities of protease and RNase increased in the course of plant development in both non-stressed and even more in stressed plants. Ca treatments of seeds or plants or their combination inhibited the decline in chlorophyll and protein contents and the rising trends of protease and RNase activities, the combined treatment being most effective. During plant development free proline content increased significantly more in water stressed plants. In non-stressed plants there was a marked increase in the free proline content at the mature fruit stage. Ca treatment inhibited the rise of free proline in stressed plants. A significant reduction in yield components and yield of the crop in water stressed plants was increased by Ca treatment.     

Heparin and heparan sulfate binding sites on B-16 melanoma cells

We have reported previously that the production of a tumor cell factor that stimulates synthesis of fibroblast collagenase is influenced by a fibroblast-deposited matrix component, possibly heparan sulfate-proteoglycan. In this study, binding sites for heparin and heparan sulfate on mouse B-16 melanoma cells have been demonstrated. Binding of 3H-heparin and 35S-heparan sulfate has been shown to occur to whole cells, isolated membranes, and to a component(s) of detergent extracts of the membranes. Scatchard analysis of binding of 3H-heparin yielded a Kd of 2-5 x 10(-8) M and a Bmax of 0.5 x 10(7) heparin molecules bound per cell. Binding of 35S-heparan sulfate was of at least an order of magnitude lower affinity than heparin, but the Bmax was similar to that for heparin. Competition studies showed that 35S-heparan sulfate binding was inhibited totally by heparin and heparan sulfate and partially by dermatan sulfate, but no inhibition was obtained with hyaluronate or chondroitin sulfate. Binding of 3H-heparin was inhibited totally by heparin but to different extents by preparations of heparan sulfate from different tissue sources. The heparin/heparan sulfate binding activity is a protein(s) because it is destroyed by treatment with trypsin. Binding of 3H-heparin to transblots of the detergent extract of the B-16 cell membranes indicated that at least part of the binding activity is a 14,000-dalton protein.     

Studies on lactic dehydrogenase and sorbitol dehydrogenase release in relation to deep freezing of buffalo semen in certain extenders

Forty seminal ejaculates from five mature buffalo bulls (n=8 from each bull), exhibiting more than 70% initial sperm motility, were frozen in the following three extenders: egg-yolk sodium citrate glycerol (EYCG); tris-egg yolk glycerol (TYG); and citric acid whey glycerol (CAWG). The extenders were evaluated for the release of intracellular enzymes, lactic dehydrogenase (LDH) and sorbitol dehydrogenase (SODH) from the spermatozoa during freezing (in fresh semen, after dilution and after equilibration) and post freezing (24 h and 7 d after freezing. It was found that the release of LDH and SODH enzymes was significantly lower in TYG than in EYCG and CAWG extenders. The most critical stage, at which the enzyme release was maximal, was between equilibration and 24 h post freezing in all three extenders.     

Pathogen-specific CD8 T cell responses are directly inhibited by IL-10

Regulation of CD8 T cell expansion and contraction is essential for successful immune defense against intracellular pathogens. IL-10 is a regulatory cytokine that can restrict T cell responses by inhibiting APC functions. IL-10, however, can also have direct effects on T cells. Although blockade or genetic deletion of IL-10 enhances T cell-mediated resistance to infections, the extent to which IL-10 limits in vivo APC function or T cell activation/proliferation remains unknown. Herein, we demonstrate that primary and memory CD8 T cell responses following Listeria monocytogenes infection are enhanced by the absence of IL-10. Surface expression of the IL-10R is transiently up-regulated on CD8 T cells following activation, suggesting that activated T cells can respond to IL-10 directly. Consistent with this notion, CD8 T cells lacking IL-10R2 underwent greater expansion than wild-type T cells upon L. monocytogenes infection. The absence of IL-10R2 on APCs, in contrast, did not enhance T cell responses following infection. Our studies demonstrate that IL-10 produced during bacterial infection directly limits expansion of pathogen-specific CD8 T cells and reveal an extrinsic regulatory mechanism that modulates the magnitude of memory T cell responses.     

Comparison of clastogenic effects of inorganic selenium salts in mice in vivo as related to concentrations and duration of exposure

Inorganic selenium compounds in the diet have been known to protect against cancer in laboratory animals, but were harmful in high concentrations. In the present work, the relative effects of two salts, sodium selenite and sodium selenate, administered to mice in vivo, in different concentrations and durations of exposure, were compared. Aqueous solutions of each salt (7, 14, 21 and 28 mg Kg^–1 bw) were fed by gavaging to mice matched in age and sex. The animals were sacrificed at intervals of 6, 12, 18 and 24 h and chromosome preparations were made following the usual schedule of colchicine-hypotonic-fixative-airdrying-Giemsa staining. The endpoints screened were chromosomal aberrations (CA) and damaged cells (DC). Both salts affected chromosome structure and spindle formation, sodium selenite being more cytotoxic than sodium selenate. The frequencies of aberrations induced were directly proportional to the concentrations used and duration of exposure.